Don't know if you ever got this figured out, but I and some others ran into the same problem (Edit bar disappearing) when linking to other js libraries. (http://www.concrete5.org/community/forums/customizing_c5/typekit_in... ) It seems to make a difference in what order the scripts are loaded -- in my case I had to put the extra js links *before* the Loader::element('header_required'); element and then the Edit bar returned and worked normally again.

You could try linking to the js files in the head of the template, rather than inside your php block at the end.